FAQ How do I remove a plug-in?

You should not remove plug-ins from Eclipse.
Plug-ins should be installed as features using the Update Manager.
The same Update Manager can be used to disable plug-ins by disabling the
feature they belong to. Run
Help > Software Updates > Manage Configuration...,
select the feature of interest, and disable it with the task shown
in the right window. In newer versions, you might need to Run
Help > About Eclipse SDK > Installation Details, and then
select the software you no longer want and click Uninstall

When a feature is disabled, all its plug-ins will be disabled also.
They are still available on disk, and they can be enabled at any
time in the future. To physically remove the feature and its plug-ins,
you will have to manually remove the feature from the eclipse/features
directory and its plug-ins from the eclipse/plugins directory. We
advise extreme caution here. Remove the wrong ones, and you may
have quite some trouble restoring your Eclipse to a stable state.
Unless you care a lot about hard disk use, we recommend
leaving the plug-ins where they are.

Comments from the peanut gallery

What about rolling back to a previous version, repairing a corrupted plugin, or eliminating conflicting plugins? Aren't there legitimate use cases for wanting to safely remove a particular plugin?

Under Helios/3.6/STS you can disable plugins at startup via "Window > Preferences" from the menu under "General > Startup and Shutdown". Uncheck the items you don't want to run when you start Eclipse.